Package org.anchoranalysis.plugin.image.task.bean.grouped

Class GroupedStackBase<S,T>

Object

AnchorBean<Task<ProvidesStackInput,GroupedSharedState<S,T>>>

Task<ProvidesStackInput,GroupedSharedState<S,T>>

GroupedStackBase<S,T>

Type Parameters:

S - individual-type

T - aggregate-type

Direct Known Subclasses:

AggregateChannelTask, ExportImageHistograms

public abstract class GroupedStackBase<S,T>
extends Task<ProvidesStackInput,GroupedSharedState<S,T>>

Base class for stacks (usually each channel from an image) that are somehow grouped-together.

Two types of entities are considered:

• The individual type, to which a Channel is converted in the image.
• The aggregated type, when multiple individual types are combined.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
GroupedStackBase()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
GroupedSharedState<S,T>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
protected abstract CheckedFunction<Channel,S,CreateException>	createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.
protected abstract GroupMapByName<S,T>	createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)	Creates a map for the storing an aggregate-data-object for each group.
void	doJobOnInput(InputBound<ProvidesStackInput,GroupedSharedState<S,T>> input)	Performs the task on a particular input.
Grouper	getGroup()	How to partition the inputs into groups.
Interpolator	getInterpolator()	The interpolator to use for scaling images.
SizeXY	getResizeTo()	If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
FromStacks	getSelectChannels()	Selects which channels are included, optionally renaming.
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
protected abstract String	outputNameForGroups()	The first-level output-name used for determining if groups are written.
protected abstract void	processIndividual(String name, S individual, boolean partOfGroup, CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual, InputOutputContext context)	Processes each derived individual element from a Channel, calling consumeIndividual one or more times.
void	setGroup(Grouper group)	How to partition the inputs into groups.
void	setInterpolator(Interpolator interpolator)	The interpolator to use for scaling images.
void	setResizeTo(SizeXY resizeTo)	If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
void	setSelectChannels(FromStacks selectChannels)	Selects which channels are included, optionally renaming.
protected abstract Optional<String>	subdirectoryForGroupOutputs()	An optional subdirectory where the group outputs are placed.

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

defaultOutputs, executeJob, isInputCompatibleWith

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

GroupedStackBase

public GroupedStackBase()

Method Details

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: Task

Highest class(es) that will function as a valid input.

This is usually the class of T (or sometimes the absolute base class InputFromManager).

Specified by:

inputTypesExpected in class Task<ProvidesStackInput,GroupedSharedState<S,T>>

Returns:

the input-types that a task expects.

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<ProvidesStackInput,GroupedSharedState<S,T>>

Returns:

true iff the execution is expected to be very quick, false otherwise.

beforeAnyJobIsExecuted

public GroupedSharedState<S,T> beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<ProvidesStackInput> inputs,
 ParametersExperiment parameters)
                                               throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<ProvidesStackInput,GroupedSharedState<S,T>>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

doJobOnInput

public void doJobOnInput(InputBound<ProvidesStackInput,GroupedSharedState<S,T>> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<ProvidesStackInput,GroupedSharedState<S,T>>

Parameters:

input - the input for the job.

Throws:

JobExecutionException - if an error occurs executing a particular job, that is not otherwise suppressed.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<ProvidesStackInput,GroupedSharedState<S,T>>

Parameters:

sharedState - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

outputNameForGroups

protected abstract String outputNameForGroups()

The first-level output-name used for determining if groups are written.

Second-level matches against this, and will determine which specific groups may or may not be written.

Returns:

the output-name.

subdirectoryForGroupOutputs

protected abstract Optional<String> subdirectoryForGroupOutputs()

An optional subdirectory where the group outputs are placed.

Returns:

an Optional containing the subdirectory name as a String, or Optional.empty() if no subdirectory is specified.

createGroupMap

protected abstract GroupMapByName<S,T> createGroupMap(ConsistentChannelChecker channelChecker,
 Optional<Stream<String>> groupIdentifiers,
 Optional<InputOutputContext> outputContext,
 OperationContext operationContext)

Creates a map for the storing an aggregate-data-object for each group.

Parameters:

channelChecker - checks that the channels of all relevant stacks have the same size and data-type.

groupIdentifiers - a stream with each group-identifier that should be added to the map.

outputContext - where to write results to when a group is processed.

operationContext - supporting entities for the operation.

Returns:

a newly created map.

createChannelDeriver

protected abstract CheckedFunction<Channel,S,CreateException> createChannelDeriver(ChannelSource source)
                                                                            throws OperationFailedException

A function to derive the individual type used for aggregation from a Channel.

Parameters:

source - how to retrieve a Channel, appropriately-sized.

Returns:

a function, that given a Channel will return an individual element of type T.

Throws:

OperationFailedException - if the channel-deriver cannot be successfully created.

processIndividual

protected abstract void processIndividual(String name,
 S individual,
 boolean partOfGroup,
 CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual,
 InputOutputContext context)
                                   throws OperationFailedException

Processes each derived individual element from a Channel, calling consumeIndividual one or more times.

Parameters:

name - the name of the channel.

individual - the derived-individual element.

partOfGroup - true when the item is part of a group, false otherwise.

consumeIndividual - a function that should be called one or more times for the individual element, or sub-elements of it.

context - supporting entities for the operation.

Throws:

OperationFailedException - if anything goes wrong during processing.

getInterpolator

public Interpolator getInterpolator()

The interpolator to use for scaling images.

setInterpolator

public void setInterpolator(Interpolator interpolator)

The interpolator to use for scaling images.

getGroup

public Grouper getGroup()

How to partition the inputs into groups.

setGroup

public void setGroup(Grouper group)

How to partition the inputs into groups.

getSelectChannels

public FromStacks getSelectChannels()

Selects which channels are included, optionally renaming.

setSelectChannels

public void setSelectChannels(FromStacks selectChannels)

Selects which channels are included, optionally renaming.

getResizeTo

public SizeXY getResizeTo()

If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).

setResizeTo

public void setResizeTo(SizeXY resizeTo)

If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).